Revision bac828e0
Added by Patrick Plitzner almost 8 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportClassification.java | ||
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| 21 | 21 |
import org.springframework.stereotype.Component; |
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|
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import eu.etaxonomy.cdm.common.CdmUtils; |
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper; |
|
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import eu.etaxonomy.cdm.io.common.DbImportBase; |
| 25 | 26 |
import eu.etaxonomy.cdm.io.common.IPartitionedIO; |
| 26 | 27 |
import eu.etaxonomy.cdm.io.common.ResultSetPartitioner; |
| ... | ... | |
| 134 | 135 |
if(parentGL!=null && parentCL!=null && parentGL.getUuid().equals(parentCL.getUuid())){
|
| 135 | 136 |
RedListUtil.logMessage(id, "Same UUID for "+parentGL+ " (Gesamtliste) and "+parentCL+" (Checkliste)", logger); |
| 136 | 137 |
} |
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|
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//add taxa for concept relationships to E, W, K, AW, AO, R, O, S |
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addTaxonToClassification(RedListUtil.uuidClassificationE, RedListUtil.CLASSIFICATION_NAMESPACE_E, id, state); |
|
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addTaxonToClassification(RedListUtil.uuidClassificationW, RedListUtil.CLASSIFICATION_NAMESPACE_W, id, state); |
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addTaxonToClassification(RedListUtil.uuidClassificationK, RedListUtil.CLASSIFICATION_NAMESPACE_K, id, state); |
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addTaxonToClassification(RedListUtil.uuidClassificationAW, RedListUtil.CLASSIFICATION_NAMESPACE_AW, id, state); |
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addTaxonToClassification(RedListUtil.uuidClassificationAO, RedListUtil.CLASSIFICATION_NAMESPACE_AO, id, state); |
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addTaxonToClassification(RedListUtil.uuidClassificationR, RedListUtil.CLASSIFICATION_NAMESPACE_R, id, state); |
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addTaxonToClassification(RedListUtil.uuidClassificationO, RedListUtil.CLASSIFICATION_NAMESPACE_O, id, state); |
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addTaxonToClassification(RedListUtil.uuidClassificationS, RedListUtil.CLASSIFICATION_NAMESPACE_S, id, state); |
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} |
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private void addTaxonToClassification(UUID classificationUuid, String classificationNamespace, long id, RedListGefaesspflanzenImportState state){
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Taxon taxon = HibernateProxyHelper.deproxy(state.getRelatedObject(classificationNamespace, String.valueOf(id), TaxonBase.class), Taxon.class); |
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Classification classification = getClassificationService().load(classificationUuid); |
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classification.addChildTaxon(taxon, null, null); |
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} |
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private void createParentChildNodes(Classification classification, long id, String gueltString, |
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportNames.java | ||
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| 103 | 103 |
|
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private void makeSingleNameAndTaxon(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonNameBase> namesToSave, Set<TaxonBase> taxaToSave) |
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throws SQLException {
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//cell values |
|
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long id = rs.getLong(RedListUtil.NAMNR); |
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String taxNameString = rs.getString(RedListUtil.TAXNAME); |
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String gueltString = rs.getString(RedListUtil.GUELT); |
| ... | ... | |
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String authorKombString = rs.getString(RedListUtil.AUTOR_KOMB); |
| 119 | 120 |
String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI); |
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String hybString = rs.getString(RedListUtil.HYB); |
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String clTaxonString = rs.getString(RedListUtil.CL_TAXON); |
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String relationE = rs.getString(RedListUtil.E); |
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String relationW = rs.getString(RedListUtil.W); |
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String relationK = rs.getString(RedListUtil.K); |
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String relationAW = rs.getString(RedListUtil.AW); |
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String relationAO = rs.getString(RedListUtil.AO); |
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String relationR = rs.getString(RedListUtil.R); |
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String relationO = rs.getString(RedListUtil.O); |
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String relationS = rs.getString(RedListUtil.S); |
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//---NAME--- |
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BotanicalName name = importName(state, id, taxNameString, rangString, ep1String, ep2String, ep3String, |
| ... | ... | |
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return; |
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} |
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/*check if taxon/synonym is also in checklist |
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* 1. create new taxon with the same name (in the checklist classification) |
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* 2. create congruent concept relationship between both |
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//---CONCEPT RELATIONSHIPS--- |
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/*check if taxon/synonym also exists in other classification |
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* 1. create new taxon with the same name (in that classification) |
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* 2. create concept relationship between both |
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*/ |
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String clTaxonString = rs.getString(RedListUtil.CL_TAXON);
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//checklist
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if(CdmUtils.isNotBlank(clTaxonString) && !clTaxonString.trim().equals("-")){
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cloneToClassification(taxonBase, name, TaxonRelationshipType.CONGRUENT_TO(), taxaToSave, id, RedListUtil.TAXON_CHECKLISTE_NAMESPACE, state); |
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} |
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cloneTaxon(taxonBase, name, TaxonRelationshipType.CONGRUENT_TO(), taxaToSave, id, RedListUtil.TAXON_CHECKLISTE_NAMESPACE, state); |
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} |
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//E, W, K, AW, AO, R, O, S |
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addConceptRelation(relationE, RedListUtil.CLASSIFICATION_NAMESPACE_E, taxonBase, name, taxaToSave, id, state); |
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addConceptRelation(relationW, RedListUtil.CLASSIFICATION_NAMESPACE_W, taxonBase, name, taxaToSave, id, state); |
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addConceptRelation(relationK, RedListUtil.CLASSIFICATION_NAMESPACE_K, taxonBase, name, taxaToSave, id, state); |
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addConceptRelation(relationAW, RedListUtil.CLASSIFICATION_NAMESPACE_AW, taxonBase, name, taxaToSave, id, state); |
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addConceptRelation(relationAO, RedListUtil.CLASSIFICATION_NAMESPACE_AO, taxonBase, name, taxaToSave, id, state); |
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addConceptRelation(relationR, RedListUtil.CLASSIFICATION_NAMESPACE_R, taxonBase, name, taxaToSave, id, state); |
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addConceptRelation(relationO, RedListUtil.CLASSIFICATION_NAMESPACE_O, taxonBase, name, taxaToSave, id, state); |
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addConceptRelation(relationS, RedListUtil.CLASSIFICATION_NAMESPACE_S, taxonBase, name, taxaToSave, id, state); |
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//NOTE: the source has to be added after cloning or otherwise the clone would also get the source |
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ImportHelper.setOriginalSource(taxonBase, state.getTransactionalSourceReference(), id, RedListUtil.TAXON_GESAMTLISTE_NAMESPACE); |
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taxaToSave.add(taxonBase); |
| 150 | 170 |
} |
| 151 | 171 |
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private void cloneToClassification(TaxonBase taxonBase, TaxonNameBase name, TaxonRelationshipType taxonRelationshipType, Set<TaxonBase> taxaToSave, long id, String sourceNameSpace, RedListGefaesspflanzenImportState state){
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private void addConceptRelation(String relationString, String classificationNamespace, TaxonBase taxonBase, TaxonNameBase name, Set<TaxonBase> taxaToSave, long id, RedListGefaesspflanzenImportState state){
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if(CdmUtils.isNotBlank(relationString) && !relationString.equals(".")){
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TaxonRelationshipType taxonRelationshipTypeByKey = new RedListGefaesspflanzenTransformer().getTaxonRelationshipTypeByKey(relationString); |
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if(taxonRelationshipTypeByKey==null){
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RedListUtil.logMessage(id, "Could not interpret relationship "+relationString+" for taxon "+taxonBase, logger); |
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} |
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cloneTaxon(taxonBase, name, taxonRelationshipTypeByKey, taxaToSave, id, classificationNamespace, state); |
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} |
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} |
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|
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private void cloneTaxon(TaxonBase taxonBase, TaxonNameBase name, TaxonRelationshipType taxonRelationshipType, Set<TaxonBase> taxaToSave, long id, String sourceNameSpace, RedListGefaesspflanzenImportState state){
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TaxonBase clone = (TaxonBase) taxonBase.clone(); |
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clone.setName(name); |
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if(taxonBase.isInstanceOf(Taxon.class)){
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenTransformer.java | ||
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| 16 | 16 |
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType; |
| 18 | 18 |
import eu.etaxonomy.cdm.model.name.Rank; |
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType; |
|
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|
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/** |
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* |
| ... | ... | |
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return null; |
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} |
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public TaxonRelationshipType getTaxonRelationshipTypeByKey(String key) {
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if (key == null){return null;}
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else {
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String substring = key.substring(key.length()-1, key.length()); |
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// if (key.equals("<")){return TaxonRelationshipType.();}//TODO: what to do here?
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if (substring.equals(">")){return TaxonRelationshipType.INCLUDES();}
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else if (substring.equals("!")){return TaxonRelationshipType.OVERLAPS();}
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else if (substring.equals("?")){return TaxonRelationshipType.ALL_RELATIONSHIPS();}
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// else if (key.equals("x")){return TaxonRelationshipType.();}//TODO: what to do here?
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} |
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return null; |
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} |
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|
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} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListUtil.java | ||
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public static final UUID uuidClassificationS = UUID.fromString("53e81162-5c2d-425b-bbe6-6e8d12e85790");
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|
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public static final String NAME_NAMESPACE = "name"; |
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public static final String AUTHOR_NAMESPACE = "author"; |
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public static final String TAXON_GESAMTLISTE_NAMESPACE = "taxon_gesamt_liste"; |
| 48 | 49 |
public static final String TAXON_CHECKLISTE_NAMESPACE = "taxon_checkliste"; |
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public static final String AUTHOR_NAMESPACE = "author"; |
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public static final String CLASSIFICATION_NAMESPACE_E = "classification_namespace_e"; |
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public static final String CLASSIFICATION_NAMESPACE_W = "classification_namespace_w"; |
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public static final String CLASSIFICATION_NAMESPACE_K = "classification_namespace_k"; |
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public static final String CLASSIFICATION_NAMESPACE_AW = "classification_namespace_aw"; |
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public static final String CLASSIFICATION_NAMESPACE_AO = "classification_namespace_ao"; |
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public static final String CLASSIFICATION_NAMESPACE_R = "classification_namespace_r"; |
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public static final String CLASSIFICATION_NAMESPACE_O = "classification_namespace_o"; |
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public static final String CLASSIFICATION_NAMESPACE_S = "classification_namespace_s"; |
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|
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|
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//cell content |
| ... | ... | |
| 85 | 93 |
public static final String CL_TAXON = "CL_TAXON"; |
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public static final String HYB = "HYB"; |
| 87 | 95 |
|
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public static final String E = "E"; |
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public static final String W = "W"; |
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public static final String K = "K"; |
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public static final String AW = "AW"; |
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public static final String AO = "AO"; |
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public static final String R = "R"; |
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public static final String O = "O"; |
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public static final String S = "S"; |
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|
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public static void logMessage(long id, String message, Logger logger){
|
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logger.error(NAMNR+": "+id+" "+message); |
| 90 | 107 |
} |
Also available in: Unified diff
Import concept relations E, W, K, AW, AO, R, O, S #5448